BMC Biology. Open Access. Abstract. BioMed Central
|
|
- Amie Dorsey
- 5 years ago
- Views:
Transcription
1 BMC Biology BioMed Central Research article The colonization of land by animals: molecular phylogeny and divergence times among arthropods Davide Pisani 1, Laura L Poling 1,2, Maureen Lyons-Weiler 1,3 and S Blair Hedges* 1 Open Access Address: 1 NASA Astrobiology Institute and Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA, 2 Dana- Farber Cancer Institute, Harvard Medical School 44 Binney Street, Boston MA 02115, USA and 3 Department of Pathology, University of Pittsburgh Medical School, 5230 Centre Avenue, Pittsburgh, PA, USA Davide Pisani - D.Pisani@nhm.ac.uk; Laura L Poling - Laura_Poling@student.hms.harvard.edu; Maureen Lyons- Weiler - mal26@pitt.edu; S Blair Hedges* - sbh1@psu.edu * Corresponding author Published: 19 January 2004 BMC Biology 2004, 2:1 This article is available from: Received: 15 October 2003 Accepted: 19 January Pisani et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. Abstract Background: The earliest fossil evidence of terrestrial animal activity is from the Ordovician, ~450 million years ago (Ma). However, there are earlier animal fossils, and most molecular clocks suggest a deep origin of animal phyla in the Precambrian, leaving open the possibility that animals colonized land much earlier than the Ordovician. To further investigate the time of colonization of land by animals, we sequenced two nuclear genes, glyceraldehyde-3-phosphate dehydrogenase and enolase, in representative arthropods and conducted phylogenetic and molecular clock analyses of those and other available DNA and protein sequence data. To assess the robustness of animal molecular clocks, we estimated the deuterostome-arthropod divergence using the arthropod fossil record for calibration and tunicate instead of vertebrate sequences to represent Deuterostomia. Nine nuclear and 15 mitochondrial genes were used in phylogenetic analyses and 61 genes were used in molecular clock analyses. Results: Significant support was found for the unconventional pairing of myriapods (millipedes and centipedes) with chelicerates (spiders, scorpions, horseshoe crabs, etc.) using nuclear and mitochondrial genes. Our estimated time for the divergence of millipedes (Diplopoda) and centipedes (Chilopoda) was 442 ± 50 Ma, and the divergence of insects and crustaceans was estimated as 666 ± 58 Ma. Our results also agree with previous studies suggesting a deep divergence (~ Ma) for arthropods and deuterostomes, considerably predating the Cambrian Explosion seen in the animal fossil record. Conclusions: The consistent support for a close relationship between myriapods and chelicerates, using mitochondrial and nuclear genes and different methods of analysis, suggests that this unexpected result is not an artefact of analysis. We propose the name Myriochelata for this group of animals, which includes many that immobilize prey with venom. Our molecular clock analyses using arthropod fossil calibrations support earlier studies using vertebrate calibrations in finding that deuterostomes and arthropods diverged hundreds of millions of years before the Cambrian explosion. However, our molecular time estimate for the divergence of millipedes and centipedes is close to the divergence time inferred from fossils. This suggests that arthropods may have adapted to the terrestrial environment relatively late in their evolutionary history. Page 1 of 10
2 Background The terrestrial environment has been greatly altered by the actions of organisms over Earth's history. Prokaryotes were probably the first organisms to colonize land, and this occurred as early as 2.6 billion years ago [1-3]. The presence of organisms on exposed land will accelerate weathering through physical and chemical processes and may in turn affect the global atmosphere and climate [4]. Therefore, it is of interest to know when different groups of organisms colonized land to better understand their effect on the biosphere. The earliest undisputed fossils of terrestrial plants, animals, and fungi are all from the early Palaeozoic (Ordovician and Silurian; million years ago, Ma) [5-9]. However, the earliest animal fossils are known from ~600 Ma [10-12] and the earliest representatives of the "plant lineage", such as green algae [13] and red algae [14], from even earlier ( Ma and 1200 Ma, respectively). This raises the possibility that land was colonized by multicellular eukaryotes prior to the Ordovician. A previous molecular clock analysis addressed the question of land colonization by plants and fungi, resulting in early time estimates of about 700 and 1000 Ma, respectively [15]. However, molecular clock analyses have not addressed the colonization of land by animals. Myriapods (centipedes, millipedes) and chelicerates (e.g., arachnids, horseshoe crabs) have figured prominently in the earliest evidence of terrestrial animals. For example, the first taxonomically identifiable body fossils of terrestrial animals are arachnids and chilopods from the late Silurian (~419 Ma) of England [6], and the oldest unambiguous evidence of sub-aerial animal activity is of arthropod (diplopod-like) trackways from ~450 Ma sediments [16]. Older arthropod traces (possibly from the latest Cambrian) have been reported from terrestrial sediments, eolian dune deposits accumulated in a sandy beach environment of southern Canada [17], although the terrestrial nature of the trace makers is uncertain. Older, marine myriapod-like fossils are known [18], but no marine remains attributable to Chilopoda or Diplopoda have been found. Here, we use molecular clock and phylogenetic methods to place temporal constraints on the early history of arthropods and the colonization of land by animals. Our focus is on the divergence of millipedes and centipedes because they represent the most ancient living lineages of terrestrial animals (based on the fossil record) whose common ancestor presumably was terrestrial. In turn, this provides a minimum estimate for the time when land was colonized by animals. With the use of a phylogenetic framework derived from analyses of all available nuclear genes, we also estimate times of other major divergences in the history of living arthropods, and the divergence of arthropods and deuterostomes. These additional data help to constrain a maximal time for the colonization of land by arthropods. Results All phylogenetic analyses resulted in significant (>95%) clustering of myriapods and chelicerates (figure 1). Pancrustacea (insects and crustaceans) was found in most analyses, the only exceptions being minimum evolution with paralinear distances, and both weighted and unweighted parsimony analyses of nuclear + mitochondrial genes, and the unweighted parsimony analysis of only nuclear genes (Table 1). However, because these exceptional analyses used models that are less complex than recommended [19], it is possible that they were influenced by substitutional biases. Support for Pancrustacea was significant in most analyses of nuclear genes and the Bayesian analysis of nuclear + mitochondrial genes. The two representative crustaceans (branchiopods and malacostracans) formed a group in the nuclear gene analysis and the Bayesian all-gene analysis. However, insects joined malacostracans in the remaining all-gene analyses. This uncertainty of relationships within Pancrustacea has been encountered previously [20] and may be related to different rates of evolution among genes. Divergence time estimates for the millipede-centipede split ranged from Ma across different molecular clock methods, with an average of 442 ± 50 Ma (Table 2). Average time estimates for the other divergences among arthropods were 475 ± 53 Ma for Xiphosura-Arachnida, 642 ± 63 Ma for Myriapoda-Chelicerata, 614 ± 23 Ma for Branchiopoda-Malacostraca, 666 ± 58 Ma for Insecta- Crustacea, and 725 ± 46 Ma for Pancrustacea-(Chelicerata-Myriapoda). As expected, the use of different calibrations resulted in different time estimates, and although the penalized likelihood method (SGG PL ) showed the greatest sensitivity to calibration differences, most methods yielded similar time estimates. The use of exclusively fossil calibration points (Chilopoda-Diplopoda, Xiphosura-Arachnida) or molecular calibration points (Arthropoda-Deuterostomia) did not result in substantially different time estimates (table 2). Therefore, time estimates using the largest number of calibration points and proteins (averaged across methods) were chosen to summarize the time of divergence for each node (Table 2, Figure 2). Using the assumption that the ancestral arthropod was aquatic (marine) and that terrestrialization is derived within arthropods, myriapods colonized land after the origin of the myriapod lineage (chelicerate-myriapod divergence; 642 ± 63 Ma) and before the millipede-centi- Page 2 of 10
3 (a) A C B Diplopoda Chilopoda Myriapoda Xiphosura Arachnida Chelicerata Myriochelata D E Insecta Branchiopoda Malacostraca Crustacea Pancrustacea Annelida 0.05 (b) A C B Diplopoda Chilopoda Xiphosura Arachnida Myriapoda Chelicerata Myriochelata Branchiopoda D Insecta Malacostraca Pancrustacea Annelida 0.05 Phylogenetic Figure 1 relationships of the arthropods Phylogenetic relationships of the arthropods (a) Minimum evolution tree of the nine concatenated nuclear genes. (b) Minimum evolution tree of the 24 concatenated nuclear and mitochondrial genes. Both trees were obtained using gamma corrected Kimura 2-parameter (transversion) distances. The same (or similar) tree topologies were obtained using other methods (Table 1). Table 1: Support values for the nodes in the phylogenetic trees (Figure 1). Numbers are posterior probabilities for Bayesian inference and bootstrap confidence values for all others methods; dashes indicate that the node was not present in the tree. Support values Data Method of analysis Node A Node B Node C Node D Node E Nuclear genes Minimum evolution (gamma, transversions) Minimum evolution (transversions) Minimum evolution (paralinear distances) Maximum likelihood Bayesian inference Maximum parsimony Weighted parsimony All genes Minimum evolution (gamma, transversions) Minimum evolution (transversions) Minimum evolution (Paralinear distances) Maximum likelihood Bayesian inference Maximum parsimony Weighted parsimony Page 3 of 10
4 Table 2: Divergence times for the major groups of arthropods. Divergence times from least squares (LS) methods are means (<30 proteins) or modes of time estimates from individual proteins. Summary times are averages across methods for comparisons that maximize the calibrations and proteins used, indicated in bold. Abbreviations: CD= Chilopoda-Diplopoda calibration (423 Ma); DA= Deuterostomia-Arthropoda calibration (993 Ma); N/A = not applicable; XA= Xiphosura-Arachnida calibration (480 Ma). Number of proteins Divergence time (Ma) and standard error (if available) Node Calibration point Total Rate constant MGG LS MGL LS SGG LS SGL LS SGL DT SGL MDT SGL PL Summary Chilopoda- Diplopoda Xiphosura- Arachnida Branchiopoda -Malacostraca Insecta- Crustacea Myriapoda- Chelicerata (Myriapoda- Chelicerata)- Pancrustacea DA ± ± ± ± ± ± ± 50 XA ± 79 N/A 357 ± 79 N/A 499 ± ± XA & DA ± ± ± ± ± ± XA &/or DA ± ± ± ± ± ± DA ± ± ± ± ± ± ± 53 CD ± 92 N/A 568 ± 92 N/A 403 ± ± CD & DA ± ± ± ± ± ± DA ± ± ± ± ± ± ± 23 XA 5 0 N/A N/A N/A N/A 680 ± ± XA & DA 5 0 N/A N/A N/A N/A 594 ± ± XA &/or DA ± ± ± ± ± ± CD 5 0 N/A N/A N/A N/A 581 ± ± XA & D 5 0 N/A N/A N/A N/A 635 ± ± CD & DA 5 0 N/A N/A N/A N/A 554 ± ± DA ± ± ± ± ± ± ± 58 XA ± 132 N/A 534 ± 132 N/A 744 ± ± XA & DA ± ± ± ± ± ± XA &/or DA ± ± ± ± ± ± CD ± 98 N/A 568 ± 98 N/A 637 ± ± XA & D ± 95 N/A 573 ± 93 N/A 695 ± ± CD & DA ± ± ± ± ± ± DA ± ± ± ± ± ± ± 63 XA ± 110 N/A 605 ± 110 N/A 751 ± ± XA & DA ± ± ± ± ± ± XA &/or DA ± ± ± ± ± ± CD ± 18 N/A 544 ± 18 N/A 640 ± ± XA & D ± 29 N/A 638 ± 29 N/A 700 ± ± CD & DA ± ± ± ± ± ± DA ± ± ± ± ± ± ± 46 XA ± 139 N/A 703 ± 139 N/A 892 ± ± XA & DA ± ± ± ± ± ± XA &/or DA ± ± ± ± ± ± CD ± 79 N/A 727 ± 79 N/A 767 ± ± XA & D ± 86 N/A 754 ± 86 N/A 836 ± ± CD & DA ± ± ± ± ± ± Page 4 of 10
5 Cambrian evolutionary explosion Proterozoic First body fossils of terrestrial arthropods Chilopoda (centipedes) Diplopoda (millipedes) Xiphosura (horseshoe crabs) Arachnida (e.g., spiders) Branchiopoda (e.g., brine shrimp) Malacostraca (e.g., crabs) Insecta (insects) Deuterostomia (e.g., vertebrates) Phanerozoic Million years ago A Figure timescale 2 of arthropod evolution A timescale of arthropod evolution Numbers associated with nodes are divergence times (Ma) and their standard errors (Table 2). Three calibration points were used: the fossil-based divergence of Chilopoda and Diplopoda (423 Ma), the fossilbased divergence of Xiphosura and Arachnida (480 Ma), and the 993 Ma deuterostome-arthropod divergence estimated from a previous molecular clock analysis. Table 3: Divergence times between Arthropoda and Deuterostomia. Times of divergence for deuterostomes and arthropods using one or both calibrations from the arthropod fossil record. Abbreviations: CD= Chilopoda-Diplopoda calibration (423 Ma); XA= Xiphosura- Arachnida calibration (480 Ma). Number of proteins Divergence times (Ma) and standard errors (if available) Deuterostom e representativ e Calibration point Total Rate constant MGG LS SGG LS SGL DT SGL MDT SGL PL Vertebrata CD ± ± ± ± XA ± ± ± ± CD & XA ± ± ± ± Tunicata CD ± ± ± ± XA ± ± ± ± CD & XA ± ± ± ± pede divergence (442 ± 50 Ma) or the earliest terrestrial fossils (~420 Ma). Time estimates for the deuterostomearthropod divergence ranged from Ma across all methods and calibrations (average of 1130 ± 120 Ma), although SGG PL gave substantially higher estimates than the other methods (Table 3). The Bayesian (SGL DT and SGL MDT ), multigene global (MGG LS ), and supergene global (SGG LS ) methods resulted in estimates of ~ Ma regardless of calibration point used or whether a vertebrate or non-vertebrate (tunicate) was used as the representative deuterostome. Page 5 of 10
6 Discussion Arthropod phylogeny A major limitation of this study, with respect to phylogenetic implications, is the sparse taxonomic sampling. As in most studies, there is a trade-off in terms of taxa and genes or proteins. In this case, we have emphasized a large number of proteins to increase the statistical resolution of relationships and time estimates at the expense of taxonomic representation. Nonetheless, our results agree with most previous molecular phylogenetic analyses in supporting a close relationship between insects and crustaceans (Pancrustacea) and between myriapods and chelicerates. Of the two groups, Pancrustacea has received the strongest support in the past [20-24]. Nonetheless, a myriapod-chelicerate grouping has been found previously with mitochondrial genes [23-25], nuclear ribosomal genes [21], and nuclear protein-coding genes [26]. Additional evidence has come from hemocyanine structure [27]. We propose the name Myriochelata (in allusion to the joining of Myriapoda and Chelicerata) for the group containing myriapods and chelicerates, which otherwise is unnamed [28]. Although we are unable to identify any morphological trait diagnostic of this clade, some trends are evident that might reflect the morphological or ecological nature of the ancestral myriochelatan. For example, many species of extant myriochelatans (e.g., spiders, scorpions, centipedes) inject and immobilize prey with a poison, albeit with structures that are not homologous. Envenomation of prey is also found among pancrustaceans, but it is less broadly distributed in that group. Certainly, envenomation has arisen multiple times in arthropods, associated mostly (but not exclusively) with terrestrial predation. The significance of this trait in arthropod evolution must await sequence evidence from a greater diversity of taxa (e.g., pycnogonids, remipedes) than is currently available, and a careful examination of the early fossil record of animals (especially from the Cambrian). In general, the difficulty in finding morphological characters diagnostic of these major clades of arthropods is probably the result of deep branching of the lineages and an early fossil record that shows great morphological diversification (the Cambrian Explosion) and some important gaps [26,29,30]. Timescale for animal evolution and colonization of land Among animals, arthropods have been considered to be the earliest colonizers of land based on fossil evidence [5-7]. However, it is possible that other animal phyla colonized land even earlier. Among them, nematodes, tardigrades, and annelids are likely candidates given their current exploitation of terrestrial environments, yet these groups have relatively poor fossil records. Determining the number of such colonization events requires a consideration of phylogeny, the fossil record, and morphological traits associated with terrestriality. For arthropods, at least four major colonization events are inferred, leading to the chilopods + diplopods, insects, arachnids, and isopod crustaceans. Additional events may have occurred in smaller lineages [24,25,31]. Moreover, the recent discovery of a basal marine hexapod fossil from the Devonian [32] suggests that some hexapod traits previously believed to have evolved as adaptations to land may have first appeared in a marine setting. Along the same lines, it is also possible that millipedes and centipedes colonized land independently. However, because the earliest fossils of those groups are presumably terrestrial [6] and our molecular time estimate is only 5% earlier than the age of those fossils, our assumption of a terrestrial common ancestor of millipedes and centipedes has little affect on the time of colonization. Our relatively young time estimates for the millipede-centipede (442 ± 50 Ma) and xiphosuran-arachnid (475 ± 53 Ma) divergences contrast with the much older time estimate for the deuterostome-arthropod divergence (~ Ma) (Tables 1 and 2). The first two are close to the corresponding fossil record estimates whereas the third one is ~400 million years earlier than the earliest fossil evidence for animals [12]. Most molecular clock analyses in the last three decades, including those using many genes, have resulted in similarly deep time estimates for the arthropod-deuterostome divergence [33]. Currently a debate exists as to whether divergences among animals are best represented by molecular clock dates or the fossil record [33-37]. The molecular clock dates suggest that early animals fossilized poorly, possibly because they were small and soft-bodied. Alternatively, others have argued that molecular time estimates are older than the true times because of statistical biases, rate changes, and calibration biases [36,38], although replies to those criticisms have been made [37]. The results of this study address several of these criticisms of molecular clocks in the following ways. (1) The time estimates reported here are not uniformly discordant with the fossil record suggesting that if statistical biases are present, they are not causing a directional and proportional bias in all time estimates. (2) Our time estimate for the deuterostome-arthropod divergence using the arthropod fossil record (exclusively) was similar to time estimates obtained in previous studies by using the vertebrate fossil record, suggesting that the vertebrate calibration is not obviously biasing time estimates. (3) Our use of tunicates instead of vertebrates for representing deuterostomes resulted in similar time estimates, further indicating that vertebrates (per se) are not causing a systematic bias in the time analysis. (4) Our use of a diversity Page 6 of 10
7 of clock methodology, including Bayesian inference and likelihood-smoothing methods, did not alter the conclusions, indicating that the global clock methods used in previous studies were not responsible for biased time estimates. (5) The use of concatenated alignments (supergenes) yielded similar results to non-concatenated (multigene) analyses, indicating that the multigene analyses of previous studies were not responsible for the discordance between molecular clocks and the fossil record. In summary, our molecular clock analysis resulted in some time estimates (e.g. millipede-centipede) in agreement with the fossil record and others (e.g., insect-crustacean) much earlier than fossil evidence (assuming that the crustaceans are, in fact, monophyletic). However, all studies, including this one, are limited by the small size of the available sequence data (5 10 proteins across major groups of arthropods). In the future, it should be possible to use several hundred proteins across a diversity of arthropod taxa, and such an analysis should greatly increase the precision of phylogenetic and molecular clock analyses. Conclusions We have found strong statistical support for the unconventional grouping of myriapods and chelicerates, a taxon that we herein name Myriochelata. We also note that many myriochelatans immobilize their prey with venom. Using only arthropod fossil calibrations, our molecular clock analyses support earlier studies that used vertebrate calibrations in finding a deep divergence of deuterostomes and arthropods, hundreds of millions of years before the Cambrian explosion. However, our much younger molecular time estimate for the millipede-centipede divergence is close to the divergence time inferred from fossils for that node. This suggests that the colonization of land by arthropods occurred relatively late in their evolutionary history. Methods Species and sequences We sequenced the protein-coding region of two nuclear glycolytic enzymes, glyceraldehyde 3-phosphate dehydrogenase (G3PDH) and enolase, in an annelid (Nereis macrydi), a mollusk (Marisa sp.; not sequenced for enolase), and eight species of arthropods: a centipede (Lithobius sp.), millipede (Diplopoda sp.), blue crab (Callinectes sapidus), brine shrimp (Artemia sp.), water flea (Daphnia magna; not sequenced in G3PDH), muscle shrimp (Ostracoda sp.; possibly Cypridopsis sp.), Atlantic horseshoe crab (Limulus polyphemus), tarantula (Phormictopus sp.), and a scorpion (Centruroides sp.). Reverse-transcriptase PCR was used to amplify and sequence (both complementary strands) a total of approximately base pairs (~363 amino acids) of the coding region of enolase and 890 base pairs (~294 amino acids) of the coding region of G3PDH. Additional sequence data were obtained from the public databases (GenBank). Genes were selected if there were nucleotide sequences available from an annelid (outgroup) and at least one representative of the following arthropod taxa: Branchiopoda (e.g., brine shrimp), Malacostraca (e.g., blue crabs), Diplopoda (e.g., millipedes), Chilopoda (e.g., centipedes), Insecta (e.g., insects), Xiphosura (e.g., horseshoe crabs), and Arachnida (e.g., spiders and scorpions). Sequences were aligned with Clustal X [39]. Additional methods and sequence accession numbers are presented elsewhere (Additional file 1). Phylogenetic methods The alignments of all nine nuclear and 15 mitochondrial genes were concatenated (Additional file 1) because individual gene data sets were, for the most part, insufficient for statistical resolution of arthropod phylogeny (Additional file 2). This required the use of exemplars (representatives) from each of the major groups. Preliminary analyses using taxa (Additional file 1) were used as a guide to choosing exemplars so that fast- or slowevolving species were not selected. Analyses of the concatenation of the nine nuclear genes, as well as a full data set of 24 genes, were carried out using minimum evolution, maximum parsimony, maximum likelihood, and Bayesian inference. Minimum evolution analyses were performed using Kimura two-parameter distances with transversions-only, gamma corrected Kimura two-parameters distances with transversionsonly, and paralinear distances. For the paralinear distance analyses, the proportion of invariable sites in the considered alignment was estimated using likelihood and assuming a HKY85 + gamma + proportion of invariable sites model of DNA evolution. Identical sites were then removed proportionally to the base frequencies estimated from all sites (PAUP default settings). Maximum parsimony analyses were carried out with an equal weighting and a 2:1 weighting scheme favoring transversions over transitions. The model used for the maximum likelihood analyses (GTR + gamma+ proportion of invariable sites) was selected using Modeltest [19], whereas Bayesian inference was carried out under mixed models, and full parameter estimation was performed during tree search for each gene. All minimum evolution analyses were performed using MEGA 2.1 [40] and PAUP [41], while likelihood and parsimony analyses, as well as the estimation of the specific gamma parameters for the minimum evolution analyses were carried out using PAUP. Bayesian analyses were performed with MrBayes 3.0 [42]. The branch and bound algorithm was used in the parsimony analyses, while in the likelihood analyses 100 heuristic searches were per- Page 7 of 10
8 formed. In the latter, starting trees were obtained using random sequence addition and swapped using the tree bisection reconnection algorithm. In the Bayesian analysis, generations were run and trees were used only after convergence was reached. Robustness for the nodes in the minimum evolution, maximum parsimony, and maximum likelihood trees was evaluated using the bootstrap. PAUP settings for the bootstrap analyses were as follows: replicates with full heuristic search (one random addition sequence) and the multiple tree option turned off. Trees were swapped using the TBR algorithm. Support for the groups recovered in the Bayesian analyses were expressed as their posterior probabilities. Gapped sites were removed prior to all analyses. Molecular clock methods Molecular clock analyses were performed using a diversity of methods [37]: multigene global least squares (MGG LS ) [43,44], multigene local least squares (MGL LS ) [45], supergene global least squares (SGG LS ) [46], supergene local least squares (SGL LS ), supergene local divtime (SGL DT ; DivTime5b) [47], supergene local multidivtime (SGL MDT ; Multidivtime) [48], and supergene local penalized likelihood (SGL PL ; r8s version 1.5) [49,50]. Least squares methods are distance based, SGL PL is a semi-parametric likelihood-smoothing method, and SGL DT and SGL MDT are Bayesian methods. Multigene methods use the mean or mode [37,44,51] of time estimates from individual proteins whereas supergene methods derive a single time estimate from the simultaneous analysis of all available proteins. SGL DT and SGL MDT are two different implementations of the Bayesian method of Thorne et al. [47]. The difference between the two being that with SGL DT protein sequences are concatenated and considered as a single entity, whereas with SGL MDT each considered protein maintains its individuality during the analyses. We used the divergence of centipedes (Chilopoda) and millipedes (Diplopoda) as the minimal (most recent) time of arthropod terrestrialization and the divergence of myriapods with their closest relatives (in this case, chelicerates) as the maximal (earliest) time for myriapod terrestrialization. The maximal time for arthropod terrestrialization was considered as the divergence between insects (Insecta) and crustaceans (Crustacea). This does not preclude the possibility that land was colonized even earlier by extinct species or groups of arthropods (or other animals). Divergence times were estimated using two calibration points from the arthropod fossil record (Additional file 1): Xiphosura-Arachnida (~480 Ma) [52] and Chilopoda- Diplopoda (423 Ma; see Additional File 1 for explanation of date) [53,54]. A third calibration point, the divergence of deuterostomes (vertebrates) and arthropods based on a molecular clock study using 50 proteins and calibrated with the vertebrate fossil record (993 Ma) [33], was used in some analyses and tested (with the arthropod fossil record and by substituting vertebrates with a tunicate, Ciona intestinalis) in others (see below). Analyses were performed using calibration points separately and simultaneously, for comparison. The millipede-centipede fossil divergence was not used to estimate the molecular clock time of that divergence. GenBank was screened for nuclear encoded proteins (>100 amino acids) in which divergence times could be estimated between two or more arthropod groups, resulting in 84 proteins. For each, reciprocal BLAST analyses were used to identify and assemble sets of available sequences, and orthology was investigated through phylogenetic analyses. In those analyses, 61 proteins ( amino acid positions) were selected for further analysis after determining that orthologous relationships (divergences corresponding to speciation events) could be distinguished from paralogous relationships (divergences corresponding to gene duplication events). The least squares-based global and local clock methods (MGG LS, SGG LS, MGL LS, SGL LS ) were performed on 49 proteins (Additional file 1) that passed the relative rate test [55] as implemented in PHYLTEST [56]. Gamma-corrected Poisson distances were used for these analyses and specific gamma parameters were estimated with PAML [57]. The Bayesian and the likelihood-smoothing local clock methods (SGL DT, SGL MDT, and SGL PL ) were used with all 61 proteins that passed or did not pass the rate tests. Branch lengths for the penalized likelihood analyses were estimated with PAML (assuming a Gamma corrected JTT model of amino acid substitution). For the Bayesian analyses, branch length estimation was performed using the software AUTOestbranches [47] in the case of SGL DT, and Estbranches [48] in the case of SGL MDT. Standard errors for SGG LS and SGL LS were calculated from amonggene comparisons (i.e., MGG LS and MGL LS ) and were not available for SGL PL. Authors' contributions DP carried out the bioinformatic research and drafted the manuscript. LLP and ML sequenced the new G3PDH and enolase sequences. LLP carried out preliminary analyses of the sequence data. SBH directed the research and assisted with drafting of the manuscript. All authors read and approved the final manuscript. Page 8 of 10
9 Additional material Additional File 1 This file (MS Word) includes: (1) additional details of the methodology, (2) accession numbers of sequences used in the phylogenetic and molecular clock analyses, (3) the aligned sequence data used in the phylogenetic analyses, and (4) additional information regarding the fossil calibration points. Click here for file [ Additional File 2 This file (pdf) contains phylogenetic trees of arthropods estimated using five representative genes. The trees were constructed with neighbor-joining, using gamma-corrected Kimura two-parameter transversion distances. Bootstrap confidence values (>50%) are shown on nodes. Click here for file [ Acknowledgements We thank Frederick Schram for helpful advice concerning arthropod taxonomy and literature. This work was supported by grants to S.B.H. from the National Science Foundation (DBI ) and the National Aeronautics and Space Administration (NCC2-1057). References 1. Horodyski RJ, Knauth LP: Life on land in the Precambrian. Science 1994, 263: Watanabe Y, Martini JEJ, Ohmoto H: Geochemical evidence for terrestrial ecosystems 2.6 billion years ago. Nature 2000, 408: Prave AR: Life on land in the Proterozoic: Evidence from the Torridonian rocks of northwest Scotland. Geology 2002, 30: Schwartzman DW: Life, temperature, and the Earth. New York, Columbia University Press; 1999: Shear WA, Bonamo PM, Grierson JD, Rolfe WDI, Smith EL, Norton RA: Early land animals in North America. Science 1984, 224: Jeram AJ, Selden PA, Edwards D: Land animals in the Silurian: arachnids and myriapods from Shropshire, England. Science 1990, 250: Gray J, Shear W: Early life on land. American Scientist 1992, 80: Redecker D, Kodner R, Graham LE: Glomalean fungi from the Ordovician. Science 2000, 289: Wellman CH, Osterloff PL, Mohluddin U: Fragments of the earliest land plants. Nature 2003, 425: Xiao SH, Zhang Y, Knoll AH: Three-dimensional preservation of algae and animal embryos in a Neoproterozoic phosphorite. Nature 1998, 391: Li CW, Chen JY, Hua TE: Precambrian sponges with cellular structures. Science 1998, 279: Barfod GH, Albarede F, Knoll AH, Xiao SH, Telouk P, Frei R, Baker J: New Lu-Hf and Pb-Pb age constraints on the earliest animal fossils. Earth Planet Sc Lett 2002, 201: Porter SM, Knoll AH: Testate amoebae in the Neoproterozoic Era: evidence from vase-shaped microfossils in the Chuar Group, Grand Canyon. Paleobiology 2000, 26: Butterfield NJ: Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 2000, 26: Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB: Molecular evidence for the early colonization of land by fungi and plants. Science 2001, 293: Johnson EW, Briggs DEG, Suthren RJ, Wright JL, Tunnicliff SP: Nonmarine arthropod traces from the subaereal Ordivician Borrowdale volcanic group, English Lake District. Geol Mag 1994, 131: MacNaughton RB, Cole JM, Dalrymple RW, Braddy SJ, Briggs DEG, Lukie TD: First steps on land: Arthropod trackways in Cambrian-Ordovician eolian sandstone, southeastern Ontario, Canada. Geology 2002, 30: Robison RA, Wiley EO: A new arthropod, Meristoma: more fallout from the Cambrian explosion. Journal of Paleontology 1995, 69: Posada D, Crandall KA: Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14: Shultz JW, Regier JC: Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade. Proc R Soc Lond B Biol Sci 2000, 267: Friedrich M, Tautz D: Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature 1995, 376: Giribet G, Edgecombe GD, Wheeler WC: Arthropod phylogeny based on eight molecular loci and morphology. Nature 2001, 413: Hwang UW, Friedrich M, Tautz D, Park CJ, Kim W: Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 2001, 413: Nardi F, Spinsanti G, Boore JL, Carapelli A, Dallai R, Frati F: Hexapod origins: monophyletic or paraphyletic? Science 2003, 299: Delsuc F, Phillips MJ, Penny D: Comment on "Hexapod origins: monophyletic or paraphyletic?". Science 2003, 301:1482; author reply Cook CE, Smith ML, Telford MJ, Bastianello A, Akam M: Hox genes and the phylogeny of the arthropods. Curr Biol 2001, 11: Kusche K, Burmester T: Diplopod hemocyanin sequence and the phylogenetic position of the Myriapoda. Mol Biol Evol 2001, 18: Štys P, Zrzavý J: Phylogeny and classification of extant Arthropoda: a review of hypotheses and nomenclature. Eur J Entomol 1994, 91: Fortey RA, Owens RM: Evolutionary radiations in the Trilobita. Major evolutionary radiations Edited by: Taylor PD and Larwood GP. Oxford, Clarendon Press; 1990: Lieberman BS: Phylogenetic analysis of some basal early Cambrian trilobites, the biogeographic origins of the Eutrilobita, and the timing of the Cambrian radiation. J Paleontol 2002, 76: Dunlop JA, Webster M: Fossil evidence, terrestrialization and arachnid phylogeny. J Arachnol 1999, 27: Haas F, Waloszek D, Hartenberger R: Devonohexapodus bocksbergensis, a new marine hexapod from the Lower Devonian Hunsrück Slates, and the origin of Atelocerata and Hexapoda. Organisms, Diversity and Evolution 2003, 3: Wang DY, Kumar S, Hedges SB: Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc R Soc Lond B Biol Sci 1999, 266: Wray GA, Levinton JS, Shapiro LH: Molecular evidence for deep Precambrian divergences among metazoan phyla. Science 1996, 274: Fortey RA, Briggs DEG, Wills MA: The Cambrian evolutionary 'explosion' recalibrated. Bioessays 1997, 19: Benton MJ, Ayala FJ: Dating the tree of life. Science 2003, 300: Hedges SB, Kumar S: Genomic clocks and evolutionary timescales. Trends in Genetics 2003, 19: Benton MJ: Early origins of modern birds and mammals: molecules vs. morphology. Bioessays 1999, 21: Thompson JD, Higgins DG, Gibson TJ: CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994, 22: Page 9 of 10
10 40. Kumar S, Tamura S, Jakobsen IB, Nei M: MEGA2: Molecular Evolutionary Genetics Analysis software. Tempe, AZ, USA, Arizona State University; Swofford DL: PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland, Massachusetts, Sinauer Associates; Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19: Hedges S. Blair, Parker Patrick H., Sibley Charles G., Kumar Sudhir: Continental breakup and the ordinal diversification of birds and mammals. Nature 1996, 381: Kumar S, Hedges SB: A molecular timescale for vertebrate evolution. Nature 1998, 392: Schubart Christoph D., Diesel Rudolf, Hedges S. Blair: Rapid evolution to terrestrial life in Jamaican crabs. Nature 1998, 393: Nei M, Xu P, Glazko G: Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proceedings of the National Academy of Sciences (U.S.A.) 2001, 98: Thorne JL, Kishino H, Painter IS: Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 1998, 15: Thorne JL, Kishino H: Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 2002, 51: Sanderson MJ: Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution 2002, 19: Sanderson MJ: r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 2003, 19: Hedges SB, Shah P: Comparison of mode estimation methods and application in molecular clock analysis. BMC Bioinformatics 2003, 4: Dunlop JA, Selden PA: The early history and phylogeny of the chelicerates. Arthropod relationships Edited by: Fortey RA and Thomas RH. London, Chapman & Hall; 1998: Almond JE: The Silurian-Devonian fossil record of the Myriapoda. Phil Trans R Soc Lond B 1985, 309: Shear WA, Selden PA: Rustling in the undergrowth: animals in early terrestrial ecosystems. Plants invade the land Edited by: Gensel PG and Edwards D. New York, Columbia University Press; 2001: Takezaki Nauko, Rzhetsky Andrey, Nei Masatoshi: Phylogenetic test of the molecular clock and linearized trees. Molecular Biology and Evolution 1995, 12: Kumar S: PHYLTEST. 2.0.th edition. University Park, PA, USA., IMEG, Department of Biology, The Pennsylvania State University; Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 1997, 13: Publish with BioMed Central and every scientist can read your work free of charge "BioMed Central will be the most significant development for disseminating the results of biomedical research in our lifetime." Sir Paul Nurse, Cancer Research UK Your research papers will be: available free of charge to the entire biomedical community peer reviewed and published immediately upon acceptance cited in PubMed and archived on PubMed Central yours you keep the copyright BioMedcentral Submit your manuscript here: Page 10 of 10
Arthropods (Arthropoda)
Arthropods (Arthropoda) Davide Pisani Laboratory of Evolutionary Biology, Department of Biology, The National University of Ireland, Maynooth, Co. Kildare, Ireland (davide. pisani@nuim.ie) Abstract Living
More informationEVOLUTION OF COMPLEX LIFE FORMS
0.002 0.6 1.0 1.9 2.8 Ancestral humans Diversification of mammals Invasion of the land Diversification of animals Origin of the major eukaryotic groups Eukaryotic cells abundant Atmospheric oxygen plentiful
More informationHexapods Resurrected
Hexapods Resurrected (Technical comment on: "Hexapod Origins: Monophyletic or Paraphyletic?") Frédéric Delsuc, Matthew J. Phillips and David Penny The Allan Wilson Centre for Molecular Ecology and Evolution
More informationDr. Amira A. AL-Hosary
Phylogenetic analysis Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic Basics: Biological
More information8/23/2014. Phylogeny and the Tree of Life
Phylogeny and the Tree of Life Chapter 26 Objectives Explain the following characteristics of the Linnaean system of classification: a. binomial nomenclature b. hierarchical classification List the major
More informationAmira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut
Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic analysis Phylogenetic Basics: Biological
More informationElements of Bioinformatics 14F01 TP5 -Phylogenetic analysis
Elements of Bioinformatics 14F01 TP5 -Phylogenetic analysis 10 December 2012 - Corrections - Exercise 1 Non-vertebrate chordates generally possess 2 homologs, vertebrates 3 or more gene copies; a Drosophila
More informationUoN, CAS, DBSC BIOL102 lecture notes by: Dr. Mustafa A. Mansi. The Phylogenetic Systematics (Phylogeny and Systematics)
- Phylogeny? - Systematics? The Phylogenetic Systematics (Phylogeny and Systematics) - Phylogenetic systematics? Connection between phylogeny and classification. - Phylogenetic systematics informs the
More informationChapters 25 and 26. Searching for Homology. Phylogeny
Chapters 25 and 26 The Origin of Life as we know it. Phylogeny traces evolutionary history of taxa Systematics- analyzes relationships (modern and past) of organisms Figure 25.1 A gallery of fossils The
More informationChapter 26: Phylogeny and the Tree of Life Phylogenies Show Evolutionary Relationships
Chapter 26: Phylogeny and the Tree of Life You Must Know The taxonomic categories and how they indicate relatedness. How systematics is used to develop phylogenetic trees. How to construct a phylogenetic
More information8/23/2014. Introduction to Animal Diversity
Introduction to Animal Diversity Chapter 32 Objectives List the characteristics that combine to define animals Summarize key events of the Paleozoic, Mesozoic, and Cenozoic eras Distinguish between the
More informationPhylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?
Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species
More informationIntegrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler Feb. 14, 2018. Phylogenetic trees VI: Dating in the 21st century: clocks, & calibrations;
More informationBioinformatics tools for phylogeny and visualization. Yanbin Yin
Bioinformatics tools for phylogeny and visualization Yanbin Yin 1 Homework assignment 5 1. Take the MAFFT alignment http://cys.bios.niu.edu/yyin/teach/pbb/purdue.cellwall.list.lignin.f a.aln as input and
More informationEffects of Gap Open and Gap Extension Penalties
Brigham Young University BYU ScholarsArchive All Faculty Publications 200-10-01 Effects of Gap Open and Gap Extension Penalties Hyrum Carroll hyrumcarroll@gmail.com Mark J. Clement clement@cs.byu.edu See
More informationUsing phylogenetics to estimate species divergence times... Basics and basic issues for Bayesian inference of divergence times (plus some digression)
Using phylogenetics to estimate species divergence times... More accurately... Basics and basic issues for Bayesian inference of divergence times (plus some digression) "A comparison of the structures
More informationPHYLOGENY AND SYSTEMATICS
AP BIOLOGY EVOLUTION/HEREDITY UNIT Unit 1 Part 11 Chapter 26 Activity #15 NAME DATE PERIOD PHYLOGENY AND SYSTEMATICS PHYLOGENY Evolutionary history of species or group of related species SYSTEMATICS Study
More informationChapter 19. History of Life on Earth
Chapter 19 History of Life on Earth Adapted from Holt Biology 2008 Chapter 19 Section 3: Evolution of Life Key Vocabulary Terms Adapted from Holt Biology 2008 Cyanobacteria Photosynthetic prokaryotes Adapted
More informationConstructing Evolutionary/Phylogenetic Trees
Constructing Evolutionary/Phylogenetic Trees 2 broad categories: istance-based methods Ultrametric Additive: UPGMA Transformed istance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood
More informationChapter Study Guide Section 17-1 The Fossil Record (pages )
Name Class Date Chapter Study Guide Section 17-1 The Fossil Record (pages 417-422) Key Concepts What is the fossil record? What information do relative dating and radioactive dating provide about fossils?
More informationChapter 16: Reconstructing and Using Phylogenies
Chapter Review 1. Use the phylogenetic tree shown at the right to complete the following. a. Explain how many clades are indicated: Three: (1) chimpanzee/human, (2) chimpanzee/ human/gorilla, and (3)chimpanzee/human/
More informationFossils Biology 2 Thursday, January 31, 2013
Fossils Biology 2 Evolution Change in the genetic composition of a group of organisms over time. Causes: Natural Selection Artificial Selection Genetic Engineering Genetic Drift Hybridization Mutation
More informationThe History of Life. Fossils and Ancient Life (page 417) How Fossils Form (page 418) Interpreting Fossil Evidence (pages ) Chapter 17
Chapter 17 The History of Life Section 17 1 The Fossil Record (pages 417 422) This section explains how fossils form and how they can be interpreted. It also describes the geologic time scale that is used
More informationb. By Proterozoic, - protected from solar radiation if about 10 M below surface of water - dominated by
I. Diversification of Life A. Review 1. Hadean Eon a. b. 2. Archaean Eon a. Earliest fossils of b. Establishment of three major domains B. Proterozoic Eon (2.5 bya - 543 mya) 1. Emergence of the a. Rock
More informationCHAPTERS 24-25: Evidence for Evolution and Phylogeny
CHAPTERS 24-25: Evidence for Evolution and Phylogeny 1. For each of the following, indicate how it is used as evidence of evolution by natural selection or shown as an evolutionary trend: a. Paleontology
More informationPHYLOGENY & THE TREE OF LIFE
PHYLOGENY & THE TREE OF LIFE PREFACE In this powerpoint we learn how biologists distinguish and categorize the millions of species on earth. Early we looked at the process of evolution here we look at
More informationChapter 26 Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life Chapter focus Shifting from the process of how evolution works to the pattern evolution produces over time. Phylogeny Phylon = tribe, geny = genesis or origin
More informationSCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION. Using Anatomy, Embryology, Biochemistry, and Paleontology
SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION Using Anatomy, Embryology, Biochemistry, and Paleontology Scientific Fields Different fields of science have contributed evidence for the theory of
More informationLetter to the Editor. Department of Biology, Arizona State University
Letter to the Editor Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well Michael S. Rosenberg and Sudhir Kumar Department of Biology, Arizona
More informationPhylogenetics. BIOL 7711 Computational Bioscience
Consortium for Comparative Genomics! University of Colorado School of Medicine Phylogenetics BIOL 7711 Computational Bioscience Biochemistry and Molecular Genetics Computational Bioscience Program Consortium
More informationAlgorithms in Bioinformatics
Algorithms in Bioinformatics Sami Khuri Department of Computer Science San José State University San José, California, USA khuri@cs.sjsu.edu www.cs.sjsu.edu/faculty/khuri Distance Methods Character Methods
More informationMETHODS FOR DETERMINING PHYLOGENY. In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task.
Chapter 12 (Strikberger) Molecular Phylogenies and Evolution METHODS FOR DETERMINING PHYLOGENY In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task. Modern
More informationPhylogenies Scores for Exhaustive Maximum Likelihood and Parsimony Scores Searches
Int. J. Bioinformatics Research and Applications, Vol. x, No. x, xxxx Phylogenies Scores for Exhaustive Maximum Likelihood and s Searches Hyrum D. Carroll, Perry G. Ridge, Mark J. Clement, Quinn O. Snell
More informationEstimating Divergence Dates from Molecular Sequences
Estimating Divergence Dates from Molecular Sequences Andrew Rambaut and Lindell Bromham Department of Zoology, University of Oxford The ability to date the time of divergence between lineages using molecular
More informationPhylogenetic relationship among S. castellii, S. cerevisiae and C. glabrata.
Supplementary Note S2 Phylogenetic relationship among S. castellii, S. cerevisiae and C. glabrata. Phylogenetic trees reconstructed by a variety of methods from either single-copy orthologous loci (Class
More informationC3020 Molecular Evolution. Exercises #3: Phylogenetics
C3020 Molecular Evolution Exercises #3: Phylogenetics Consider the following sequences for five taxa 1-5 and the known outgroup O, which has the ancestral states (note that sequence 3 has changed from
More informationEfficiencies of maximum likelihood methods of phylogenetic inferences when different substitution models are used
Molecular Phylogenetics and Evolution 31 (2004) 865 873 MOLECULAR PHYLOGENETICS AND EVOLUTION www.elsevier.com/locate/ympev Efficiencies of maximum likelihood methods of phylogenetic inferences when different
More informationPhylogeny is the evolutionary history of a group of organisms. Based on the idea that organisms are related by evolution
Bio 1M: Phylogeny and the history of life 1 Phylogeny S25.1; Bioskill 11 (2ndEd S27.1; Bioskills 3) Bioskills are in the back of your book Phylogeny is the evolutionary history of a group of organisms
More informationConcepts and Methods in Molecular Divergence Time Estimation
Concepts and Methods in Molecular Divergence Time Estimation 26 November 2012 Prashant P. Sharma American Museum of Natural History Overview 1. Why do we date trees? 2. The molecular clock 3. Local clocks
More informationBiology. Slide 1 of 40. End Show. Copyright Pearson Prentice Hall
Biology 1 of 40 2 of 40 Fossils and Ancient Life What is the fossil record? 3 of 40 Fossils and Ancient Life The fossil record provides evidence about the history of life on Earth. It also shows how different
More informationInDel 3-5. InDel 8-9. InDel 3-5. InDel 8-9. InDel InDel 8-9
Lecture 5 Alignment I. Introduction. For sequence data, the process of generating an alignment establishes positional homologies; that is, alignment provides the identification of homologous phylogenetic
More informationAP Biology. Cladistics
Cladistics Kingdom Summary Review slide Review slide Classification Old 5 Kingdom system Eukaryote Monera, Protists, Plants, Fungi, Animals New 3 Domain system reflects a greater understanding of evolution
More informationWhat is Phylogenetics
What is Phylogenetics Phylogenetics is the area of research concerned with finding the genetic connections and relationships between species. The basic idea is to compare specific characters (features)
More informationChapter 22: Descent with Modification 1. BRIEFLY summarize the main points that Darwin made in The Origin of Species.
AP Biology Chapter Packet 7- Evolution Name Chapter 22: Descent with Modification 1. BRIEFLY summarize the main points that Darwin made in The Origin of Species. 2. Define the following terms: a. Natural
More informationChapter 26 Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence
More informationRadiation and Evolution of Metazoans: The Cambrian Explosion and the Burgess Shale Fossils. Geology 331, Paleontology
Radiation and Evolution of Metazoans: The Cambrian Explosion and the Burgess Shale Fossils Geology 331, Paleontology Marshall, 2006 Halkierids, which produced some of the small, shelly fossils of the Early
More informationConstructing Evolutionary/Phylogenetic Trees
Constructing Evolutionary/Phylogenetic Trees 2 broad categories: Distance-based methods Ultrametric Additive: UPGMA Transformed Distance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood
More informationSection 17 1 The Fossil Record (pages )
Chapter 17 The History of Life Section 17 1 The Fossil Record (pages 417 422) Key Concepts What is the fossil record? What information do relative dating and radioactive dating provide about fossils? What
More informationPhylogenetic Tree Reconstruction
I519 Introduction to Bioinformatics, 2011 Phylogenetic Tree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & Computing, IUB Evolution theory Speciation Evolution of new organisms is driven
More informationOrigins of Life and Extinction
Origins of Life and Extinction What is evolution? What is evolution? The change in the genetic makeup of a population over time Evolution accounts for the diversity of life on Earth Natural selection is
More informationLecture 11 Friday, October 21, 2011
Lecture 11 Friday, October 21, 2011 Phylogenetic tree (phylogeny) Darwin and classification: In the Origin, Darwin said that descent from a common ancestral species could explain why the Linnaean system
More informationBio94 Discussion Activity week 3: Chapter 27 Phylogenies and the History of Life
Bio94 Discussion Activity week 3: Chapter 27 Phylogenies and the History of Life 1. Constructing a phylogenetic tree using a cladistic approach Construct a phylogenetic tree using the following table:
More informationAssessing an Unknown Evolutionary Process: Effect of Increasing Site- Specific Knowledge Through Taxon Addition
Assessing an Unknown Evolutionary Process: Effect of Increasing Site- Specific Knowledge Through Taxon Addition David D. Pollock* and William J. Bruno* *Theoretical Biology and Biophysics, Los Alamos National
More informationHexapoda Origins: Monophyletic, Paraphyletic or Polyphyletic? Rob King and Matt Kretz
Hexapoda Origins: Monophyletic, Paraphyletic or Polyphyletic? Rob King and Matt Kretz Outline Review Hexapod Origins Response to Hexapod Origins How the same data = different trees Arthropod Origins The
More informationThe Evolutionary History of the Animal Kingdom
The Evolutionary History of the Animal Kingdom Bởi: OpenStaxCollege Many questions regarding the origins and evolutionary history of the animal kingdom continue to be researched and debated, as new fossil
More informationGenomes and Their Evolution
Chapter 21 Genomes and Their Evolution PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More information17-1 The Fossil Record Slide 1 of 40
1 of 40 Fossils and Ancient Life Fossils and Ancient Life Paleontologists are scientists who collect and study fossils. All information about past life is called the fossil record. The fossil record includes
More informationAP: CHAPTER 24: THE ORIGIN OF SPECIES 1. Define the term species.
AP Biology Chapter 24 Guided Reading Assignment Ms. Hall Name AP: CHAPTER 24: THE ORIGIN OF SPECIES 1. Define the term species. 2. How do the patterns of speciation differ? a. anagenesis b. cladogenesis
More informationName Class Date. Crossword Puzzle Use the clues below to complete the puzzle.
Chapter 17 The History of Life Chapter Vocabulary Review Crossword Puzzle Use the clues below to complete the puzzle. 1 2 3 4 5 6 7 8 9 10 11 Across 2. time span shorter than an era, such as Quaternary
More informationBINF6201/8201. Molecular phylogenetic methods
BINF60/80 Molecular phylogenetic methods 0-7-06 Phylogenetics Ø According to the evolutionary theory, all life forms on this planet are related to one another by descent. Ø Traditionally, phylogenetics
More informationPhylogeny 9/8/2014. Evolutionary Relationships. Data Supporting Phylogeny. Chapter 26
Phylogeny Chapter 26 Taxonomy Taxonomy: ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences Carolus Linnaeus developed binomial nomenclature,
More informationChapter 19 Organizing Information About Species: Taxonomy and Cladistics
Chapter 19 Organizing Information About Species: Taxonomy and Cladistics An unexpected family tree. What are the evolutionary relationships among a human, a mushroom, and a tulip? Molecular systematics
More informationHillis DM Inferring complex phylogenies. Nature 383:
Hillis DM. 1996. Inferring complex phylogenies. Nature 383: 130-131. Triangles: parsimony Squares: neighbor-joining (under specified model) Circles: UPGMA Designing your phylogenetic analysis Choice of
More informationMOLECULAR PHYLOGENY AND GENETIC DIVERSITY ANALYSIS. Masatoshi Nei"
MOLECULAR PHYLOGENY AND GENETIC DIVERSITY ANALYSIS Masatoshi Nei" Abstract: Phylogenetic trees: Recent advances in statistical methods for phylogenetic reconstruction and genetic diversity analysis were
More informationLecture V Phylogeny and Systematics Dr. Kopeny
Delivered 1/30 and 2/1 Lecture V Phylogeny and Systematics Dr. Kopeny Lecture V How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics Textbook Reading: pp 425-433, 435-437
More informationMolecular phylogeny - Using molecular sequences to infer evolutionary relationships. Tore Samuelsson Feb 2016
Molecular phylogeny - Using molecular sequences to infer evolutionary relationships Tore Samuelsson Feb 2016 Molecular phylogeny is being used in the identification and characterization of new pathogens,
More informationName. Ecology & Evolutionary Biology 2245/2245W Exam 2 1 March 2014
Name 1 Ecology & Evolutionary Biology 2245/2245W Exam 2 1 March 2014 1. Use the following matrix of nucleotide sequence data and the corresponding tree to answer questions a. through h. below. (16 points)
More informationReconstructing the history of lineages
Reconstructing the history of lineages Class outline Systematics Phylogenetic systematics Phylogenetic trees and maps Class outline Definitions Systematics Phylogenetic systematics/cladistics Systematics
More informationWarm-Up- Review Natural Selection and Reproduction for quiz today!!!! Notes on Evidence of Evolution Work on Vocabulary and Lab
Date: Agenda Warm-Up- Review Natural Selection and Reproduction for quiz today!!!! Notes on Evidence of Evolution Work on Vocabulary and Lab Ask questions based on 5.1 and 5.2 Quiz on 5.1 and 5.2 How
More information17-1 The Fossil Record Slide 2 of 40
2 of 40 Fossils and Ancient Life What is the fossil record? 3 of 40 Fossils and Ancient Life Fossils and Ancient Life Paleontologists are scientists who collect and study fossils. All information about
More information"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky
MOLECULAR PHYLOGENY "Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky EVOLUTION - theory that groups of organisms change over time so that descendeants differ structurally
More informationPhylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More informationBio 2 Plant and Animal Biology
Bio 2 Plant and Animal Biology Evolution Evolution as the explanation for life s unity and diversity Darwinian Revolution Two main Points Descent with Modification Natural Selection Biological Species
More informationBio 1B Lecture Outline (please print and bring along) Fall, 2007
Bio 1B Lecture Outline (please print and bring along) Fall, 2007 B.D. Mishler, Dept. of Integrative Biology 2-6810, bmishler@berkeley.edu Evolution lecture #5 -- Molecular genetics and molecular evolution
More informationPhylogenetic inference
Phylogenetic inference Bas E. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, March 7 th 016 After this lecture, you can discuss (dis-) advantages of different information types
More informationAnimal Diversity. Features shared by all animals. Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers
Animal Diversity Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers Nutritional mode Ingest food and use enzymes in the body to digest Cell structure and
More informationBiology 211 (2) Week 1 KEY!
Biology 211 (2) Week 1 KEY Chapter 1 KEY FIGURES: 1.2, 1.3, 1.4, 1.5, 1.6, 1.7 VOCABULARY: Adaptation: a trait that increases the fitness Cells: a developed, system bound with a thin outer layer made of
More informationName: Class: Date: ID: A
Class: _ Date: _ Ch 17 Practice test 1. A segment of DNA that stores genetic information is called a(n) a. amino acid. b. gene. c. protein. d. intron. 2. In which of the following processes does change
More informationThis is a repository copy of Microbiology: Mind the gaps in cellular evolution.
This is a repository copy of Microbiology: Mind the gaps in cellular evolution. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/114978/ Version: Accepted Version Article:
More informationPhylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from
More informationPhylogeny & Systematics
Phylogeny & Systematics Phylogeny & Systematics An unexpected family tree. What are the evolutionary relationships among a human, a mushroom, and a tulip? Molecular systematics has revealed that despite
More informationEvolution and diversity of organisms
Evolution and diversity of organisms Competency Levels - 7 3.1.1 Uses the theories of origin of life and natural selection to analyze the process of evolution of life 3.2.1 Constructs hierarchy of taxa
More informationSection 17 1 The Fossil Record (pages )
Name Class Date Chapter 17 The History of Life Section 17 1 The Fossil Record (pages 417 422) This section explains how fossils form and how they can be interpreted. It also describes the geologic time
More informationPhylogenetics in the Age of Genomics: Prospects and Challenges
Phylogenetics in the Age of Genomics: Prospects and Challenges Antonis Rokas Department of Biological Sciences, Vanderbilt University http://as.vanderbilt.edu/rokaslab http://pubmed2wordle.appspot.com/
More informationHistory of Life on Earth The Geological Time- Scale
History of Life on Earth The Geological Time- Scale Agenda or Summary Layout The Geological Time-Scale 1 2 3 The Geological Time-Scale The Beginning of Life Cambrian Explosion The Geological Time-Scale
More informationClassification and Phylogeny
Classification and Phylogeny The diversity of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize without a scheme
More informationBiodiversity. The Road to the Six Kingdoms of Life
Biodiversity The Road to the Six Kingdoms of Life How the 6 kingdoms came about At first, only two kingdoms were recognized Then Haeckel proposed a third kingdom Protista (where protists had both plant
More informationSPECIATION. REPRODUCTIVE BARRIERS PREZYGOTIC: Barriers that prevent fertilization. Habitat isolation Populations can t get together
SPECIATION Origin of new species=speciation -Process by which one species splits into two or more species, accounts for both the unity and diversity of life SPECIES BIOLOGICAL CONCEPT Population or groups
More informationUnit 7: Evolution Guided Reading Questions (80 pts total)
AP Biology Biology, Campbell and Reece, 10th Edition Adapted from chapter reading guides originally created by Lynn Miriello Name: Unit 7: Evolution Guided Reading Questions (80 pts total) Chapter 22 Descent
More informationAnimal Diversity. Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers 9/20/2017
Animal Diversity Chapter 32 Which of these organisms are animals? Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers Animals share the same: Nutritional
More informationThe Tempo of Macroevolution: Patterns of Diversification and Extinction
The Tempo of Macroevolution: Patterns of Diversification and Extinction During the semester we have been consider various aspects parameters associated with biodiversity. Current usage stems from 1980's
More informationPhylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline
Phylogenetics Todd Vision iology 522 March 26, 2007 pplications of phylogenetics Studying organismal or biogeographic history Systematics ating events in the fossil record onservation biology Studying
More informationB. Phylogeny and Systematics:
Tracing Phylogeny A. Fossils: Some fossils form as is weathered and eroded from the land and carried by rivers to seas and where the particles settle to the bottom. Deposits pile up and the older sediments
More informationOrigins of Life. Fundamental Properties of Life. Conditions on Early Earth. Evolution of Cells. The Tree of Life
The Tree of Life Chapter 26 Origins of Life The Earth formed as a hot mass of molten rock about 4.5 billion years ago (BYA) -As it cooled, chemically-rich oceans were formed from water condensation Life
More informationClassification and Phylogeny
Classification and Phylogeny The diversity it of life is great. To communicate about it, there must be a scheme for organization. There are many species that would be difficult to organize without a scheme
More informationThe Phylogenetic Handbook
The Phylogenetic Handbook A Practical Approach to DNA and Protein Phylogeny Edited by Marco Salemi University of California, Irvine and Katholieke Universiteit Leuven, Belgium and Anne-Mieke Vandamme Rega
More informationModern Evolutionary Classification. Section 18-2 pgs
Modern Evolutionary Classification Section 18-2 pgs 451-455 Modern Evolutionary Classification In a sense, organisms determine who belongs to their species by choosing with whom they will mate. Taxonomic
More informationThe practice of naming and classifying organisms is called taxonomy.
Chapter 18 Key Idea: Biologists use taxonomic systems to organize their knowledge of organisms. These systems attempt to provide consistent ways to name and categorize organisms. The practice of naming
More informationAn Introduction to the Invertebrates
An Introduction to the Invertebrates Janet Moore New Hall, Cambridge niustrations by Raith Overhill Second Edition. :::.. CAMBRIDGE :: UNIVERSITY PRESS ~nts ao Paulo, Delhi rcss, New York._ MOO 586 List
More informationReview Dating branches on the Tree of Life using DNA Gregory A Wray
http://genomebiology.com/2001/3/1/reviews/0001.1 Review Dating branches on the Tree of Life using DNA Gregory A Wray Address: Department of Biology, Duke University, Durham, NC 27708-0338, USA. E-mail:
More information